6-58275476-A-T

Variant names:

• chr6-58275476-A-T
• rs1850417
• ENST00000641631.1:n.291-25263A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641631.1(ENSG00000225096):​n.291-25263A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,054 control chromosomes in the GnomAD database, including 64,216 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64216 hom., cov: 31)
• Consequence: ENSG00000225096 ENST00000641631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225096	ENST00000641631.1	n.291-25263A>T		intron_variant	Intron 3 of 6
ENSG00000225096	ENST00000641775.1	n.456+112727A>T		intron_variant	Intron 4 of 5
ENSG00000225096	ENST00000661843.1	n.341-34820A>T		intron_variant	Intron 4 of 6
ENSG00000225096	ENST00000670654.1	n.449-79669A>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139398 AN: 151936 Hom.: 64153 Cov.: 31

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.913

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.918 AC: 139520 AN: 152054 Hom.: 64216 Cov.: 31 AF XY: 0.917 AC XY: 68110 AN XY: 74314

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.914

Alfa AF: 0.870 Hom.: 2750

Bravo AF: 0.924

Asia WGS AF: 0.986 AC: 3426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1850417; hg19: chr6-58601754;